Nucleic acid solvation: from outside to insight Pascal Auffinger and Yaser Hashem Nucleic acids are polyanionic molecules that were historically considered to be solely surrounded by a shell of water molecules and a neutralizing cloud of monovalent and divalent cations. In this respect, recent experimental and theoretical reports demonstrate that water molecules within complex nucleic acid structures can display very long residency times, and assist drug binding and catalytic reactions. Finally, anions can also bind to these polyanionic systems. Many of these recent insights are provided by state-of-the-art molecular dynamics simulations of nucleic acid systems, which will be described together with relevant methodological issues. Addresses Architecture et re ´ activite ´ de l’ARN, Universite ´ Louis Pasteur de Strasbourg, CNRS, IBMC, 15 rue Rene ´ Descartes, 67084 Strasbourg, France Corresponding author: Auffinger, Pascal (p.auffinger@ibmc.u-strasbg.fr) Current Opinion in Structural Biology 2007, 17:325–333 This review comes from a themed issue on Nucleic acids Edited by Dinshaw J Patel and Eric Westhof Available online 15th June 2007 0959-440X/$ – see front matter # 2007 Elsevier Ltd. All rights reserved. DOI 10.1016/j.sbi.2007.05.008 Introduction A thorough description of the structure of the solvent shells surrounding nucleic acid systems is important for understanding most molecular recognition processes, ran- ging from folding and assembly of proteins and nucleic acids to the binding of small ligands. To investigate these subtle aspects, molecular dynamics (MD) simulations are a technique of choice that confirms the inspiring, exper- imentally supported, intuitive statement that ‘water is an integral part of nucleic acids’ [1,2]. In this respect, water and also ions are observed to contact nucleic acid struc- tures not only on the ‘outside’, by neutralizing the nega- tive charges carried by the phosphate groups, but also to penetrate ‘inside’ the structures, where they are observed in grooves and can occupy well-defined and structurally important binding pockets [3]. Hence, it became appar- ent that monovalent ions play a role that cannot easily be overlooked. Some of the most recent theoretical MD studies related to this topic will be addressed in this review, with the hope of providing ‘insights’ into the various roles played by the solvent in biomolecular sys- tems. A list of all MD simulations of RNA systems with explicit representations of the solvent, up to October 2005, is available in [4  ]. Two accounts related to RNA enzymatic reactions from an experimental [5] and theoretical [6  ] perspective have recently been published. Several reviews and a book [7] on MD simulations [8  ,9] and on the solvation of nucleic acids [10–12] are also likely to be of interest to the reader. Solvent: a structure-stabilizing component and a guide to folding Water It is now well accepted that solvent plays a key role in the stabilization of biomolecular systems in general and nucleic acids in particular. This has been very nicely exemplified by some of the first nucleic acid MD simu- lations that explicitly took into account the solvent. For instance, an MD simulation of a DNA dodecamer in in vacuo conditions (absence of solvent) revealed rapid unstructuring of the duplex on a 100 ps timescale. How- ever, when explicit solvent particles were taken into account, the stability of the system increased signifi- cantly, emphasizing the structural role of the solvent [13]. Hence, in silico experiments in which interactions associated with important components of natural systems are switched off (in vacuo) or on (in aquo) illustrate the usefulness of MD techniques in evaluating the effects linked to the presence or absence of the solvent. Similar conclusions could be drawn from in silico exper- iments in which the effects related to long-range electro- static interactions were evaluated. These simulations demonstrated that the inclusion of long-range inter- actions involving the solvent contributed decisively to the stability of nucleic acid systems. Neglecting them leads to rapid unfolding of key structural motifs, such as tRNA hairpin loops [14,15]. These interactions, also called hydration or solvation forces [16], play a key role in the statics and dynamics of biomolecular systems. Recent studies exemplified the role of the solvent in the folding of proteins [17  ] and nucleic acids [18  ], proposed that ‘‘biomolecules have evolved to use water to help guide folding’’, and suggested that long-range water- mediated potentials assist folding by smoothing the underlying folding funnel [19,20]. For instance, ensemble MD simulations, with nearly 500 ms of aggregate simu- lation time, using an explicit representation of the ionic solvent suggested that it is necessary to account www.sciencedirect.com Current Opinion in Structural Biology 2007, 17:325–333